Project Viva: Age 7 DNAm and metals EWAS

Required Packages and functions

# libraries
library(sas7bdat)
library(sva)
library(reshape)
library(ggplot2)
library(gridExtra)
library(knitr)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(minfi)
library(stringr)
library(limma)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(minfi)
library(DMRcate)
library(UpSetR)
library(reshape)
library(corrplot)
library(factoextra)
library(ENmix)

# loading annotation
anno = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
anno = data.frame(anno)

# loading functions
setwd('/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local')
source('EWAS functions.R')

Load DNAm and pheno data

# infants with cord blood data
load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/CordBlood_ComBat_Betas_Mvals_filteredProbes_metalAnalysis.RData")
rm(ComBat.Mvalues.Metals, ComBat.Betas.Metals);gc()

# age 7 data
load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/Age7Blood_ComBat_Betas_Mvals_filteredProbes_metalAnalaysis.RData")

dim(pDatAge7Metal)
# 333 164

dim(ComBat.Mvalues.Metals)
# 394460    333

rownames(pDatAge7Metal) = pDatAge7Metal$samplename

pDatAge7Metal$age_yrs_7y_blood = pDatAge7Metal$c_age_days_7y_blood/365

# smoking 
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'xnever'] = 0
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'former'] = 1
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'smoke preg'] = 2
pDatAge7Metal$smk_preg2 = factor(pDatAge7Metal$smk_preg2)

# pheno with overlap between cord blood and age 7
pDatAge7Metal_cord = pDatAge7Metal[pDatAge7Metal$alias %in% pDatcordMetal$alias,]
dim(pDatAge7Metal_cord)
# 189 166

EWAS

As

DMP_As_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk')
 
# Unadjusted, N =  333 
# Unadjusted, p<0.05:  23361 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15990 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9130156 
 
# Number of DMRs identified:   5 

DMP_As_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_As_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  17770 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9489588 
 
# Number of DMRs identified:   7 

rm(DMP_As_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
2	113992761	113993313	0	552	0	0.00e+00	8
3	46759437	46759698	0	261	0	8.00e-07	7
1	228395659	228396009	0	350	0	7.00e-07	5
17	1395863	1396123	0	260	0	2.00e-06	5
17	75315485	75315667	0	182	0	2.62e-05	6

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_manhattan_DMP_adj.png")

As, female

pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))

DMP_As_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26064 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16222 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9159963 

# Number of DMRs identified:   4 

DMP_As_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
pDatAge7Metal_F_cord = pDatAge7Metal_cord[pDatAge7Metal_cord$female_d == 1,]
pDatAge7Metal_F_cord$race_child2 = as.factor(as.numeric(pDatAge7Metal_F_cord$race_child2))

DMP_As_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  16601 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9435264 
 
# Number of DMRs identified:   2 

rm(DMP_As_F_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
7	76027000	76027101	0.0e+00	101	0.0e+00	0.0000017	3
1	11561496	11561711	0.0e+00	215	0.0e+00	0.0000058	3
2	113992842	113993142	0.0e+00	300	0.0e+00	0.0000341	5
2	198651075	198651347	8.8e-06	272	8.8e-06	0.0127295	3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_manhattan_DMP_adj.png")

As, male

pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))

DMP_As_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  11497 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13972 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8382292 
 
# Number of DMRs identified:   4 

DMP_As_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
pDatAge7Metal_M_cord = pDatAge7Metal_cord[pDatAge7Metal_cord$female_d == 0,]
pDatAge7Metal_M_cord$race_child2 = as.factor(as.numeric(pDatAge7Metal_M_cord$race_child2))

DMP_As_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  17353 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9654988 
 
# Number of DMRs identified:   7 

rm(DMP_As_M_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	47091977	47092178	0e+00	201	0e+00	0.0000001	4
8	22735275	22735478	0e+00	203	1e-07	0.0000619	4
2	164204751	164205032	1e-07	281	1e-07	0.0001212	4
16	88706240	88706389	8e-07	149	8e-07	0.0021312	2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_manhattan_DMP_adj.png")

Ba

DMP_Ba_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk')

Unadjusted, N =  333 
Unadjusted, p<0.05:  11801 
Unadjusted, FDR<0.05:  0 
Unadjusted, pBonf<0.05:  0 
 
Adjusted, N =  333 
Adjusted, p<0.05:  12058 
Adjusted, FDR<0.05:  0 
Adjusted, pBonf<0.05:  0 
Adjusted, lambda:  0.7933736 
 
Number of DMRs identified:   3 

DMP_Ba_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  14226 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8384028 
 
# Number of DMRs identified:   4 

rm(DMP_Ba_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	6899084	6899577	0	493	0	0.0e+00	10
6	32145349	32145923	0	574	0	4.0e-07	20
16	1583809	1584118	0	309	0	4.6e-06	6

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, female

DMP_Ba_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  29651 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  23980 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.210756 
 
# Number of DMRs identified:   6

DMP_Ba_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  26653 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.238713 
 
# Number of DMRs identified:   4 

rm(DMP_Ba_F_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	6899084	6899577	0.0000000	493	0.0000000	0.0000000	10
17	37123637	37123949	0.0000000	312	0.0000000	0.0000011	9
22	30476088	30476345	0.0000000	257	0.0000001	0.0000450	8
2	183943387	183943551	0.0000000	164	0.0000001	0.0000863	5
8	144635308	144635610	0.0000005	302	0.0000005	0.0005899	8
7	94285269	94285288	0.0011747	19	0.0011747	1.0000000	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, male

DMP_Ba_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  25363 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  25117 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.190464 
 
# Number of DMRs identified:   3 

DMP_Ba_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  15406 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9304526 
 
# Number of DMRs identified:   2 

rm(DMP_Ba_M_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
16	1583809	1584118	0e+00	309	0e+00	0.0000000	6
19	50194119	50194252	0e+00	133	0e+00	0.0000061	5
6	29595001	29595335	1e-07	334	1e-07	0.0001585	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_manhattan_DMP_adj.png")

Cd

DMP_Cd_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  9428 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11898 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.8219919 
 
# Number of DMRs identified:   3 

DMP_Cd_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  14918 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9046147 
 
# Number of DMRs identified:   3 

rm(DMP_Cd_age7_cordoverlap)

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
112561	cg07044523	0.26 (0.17 ,0.34)	5.28	0	0.0021538	0.0022	chr1	153514376	S100A5

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
7	158045979	158046166	0	187	0	6.7e-06	3
5	23507449	23507656	0	207	0	9.6e-06	5
17	46685291	46685448	0	157	0	5.6e-05	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, female

DMP_Cd_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  13276 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  13415 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8339903 
 
# Number of DMRs identified:   6

DMP_Cd_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  17304 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9489797 
 
# Number of DMRs identified:   7 

rm(DMP_Cd_F_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	32164926	32165321	0.0000000	395	0.0000000	0.0000000	7
17	46685291	46685448	0.0000000	157	0.0000000	0.0000008	5
6	1624385	1624442	0.0000001	57	0.0000001	0.0003821	2
5	23507449	23507656	0.0000001	207	0.0000001	0.0001196	5
11	73357094	73357276	0.0000020	182	0.0000025	0.0044181	6
5	132113754	132113860	0.0179428	106	0.0179428	1.0000000	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, male

DMP_Cd_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16666 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  21565 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.111181 
 
# Number of DMRs identified:   3 

# DMP_Cd_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  22052 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.140586 
 
# Number of DMRs identified:   1 

rm(DMP_Cd_M_age7_cordoverlap)

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	61446961	61447369	0.00e+00	408	0.00e+00	0.0000000	11
7	50518572	50518647	1.80e-06	75	2.80e-06	0.0096276	2
6	28446839	28447087	6.28e-05	248	6.28e-05	0.0951117	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_manhattan_DMP_adj.png")

Cr

DMP_Cr_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  29723 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23609 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.115003 
 
# Number of DMRs identified:   5 

DMP_Cr_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  19986 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.050624 
 
# Number of DMRs identified:   4 

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
5	145758709	145758881	0.00e+00	172	0.00e+00	0.0000182	4
16	66969473	66969500	0.00e+00	27	1.00e-07	0.0003708	2
6	33245769	33245990	7.00e-07	221	1.10e-06	0.0012157	7
19	50666378	50666538	2.37e-05	160	2.74e-05	0.0567867	3
6	33280198	33280228	2.74e-05	30	2.74e-05	0.3024815	3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, female

DMP_Cr_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26701 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  24909 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.186951 
 
# Number of identified DMR:  0

DMP_Cr_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  29235 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.299635 
 
# Number of identified DMR:  0

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, male

DMP_Cr_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  17887 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12574 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8769853 
 
# Number of DMRs identified:   1

DMP_Cr_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  14324 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.874334 
 
# Number of DMRs identified:   1 

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	46685291	46685448	0	157	0	1.8e-06	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_manhattan_DMP_adj.png")

Cs

DMP_Cs_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  16687 
# Unadjusted, FDR<0.05:  4 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  13318 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8387198 
 
# Number of DMRs identified:   5 

DMP_Cs_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  13290 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8376426 
 
# Number of DMRs identified:   5 

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
13	47472049	47472429	0.0000000	380	0.0000001	0.0000226	12
6	33280051	33280228	0.0000000	177	0.0000001	0.0000553	6
10	94820922	94821085	0.0000001	163	0.0000001	0.0001480	6
6	32847761	32847845	0.0000449	84	0.0000561	0.1900047	7
20	57427641	57427762	0.0010524	121	0.0010524	0.9677029	6

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, female

DMP_Cs_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  25871 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16348 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9656277 
 
# Number of DMRs identified:   3 

DMP_Cs_F_age7[[3]]= NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  12170 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7999635 
 
# Number of DMRs identified:   2 

rm(DMP_Cs_F_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
1	200272111	200272215	0	104	0	2.10e-05	3
20	3145355	3145597	0	242	0	1.32e-05	3
6	29648378	29648628	0	250	0	3.89e-05	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, male

DMP_Cs_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk')

Unadjusted, N =  175 
Unadjusted, p<0.05:  15896 
Unadjusted, FDR<0.05:  0 
Unadjusted, pBonf<0.05:  0 
 
Adjusted, N =  175 
Adjusted, p<0.05:  15716 
Adjusted, FDR<0.05:  0 
Adjusted, pBonf<0.05:  0 
Adjusted, lambda:  0.9276189 
 
Number of DMRs identified:   1 
 
DMP_Cs_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  15813 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8980376 
 
# Number of DMRs identified:   10 

rm(DMP_Cs_M_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	57427555	57427762	1.86e-05	207	1.86e-05	0.0347322	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_manhattan_DMP_adj.png")

Cu

DMP_Cu_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  10199 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20001 
# Adjusted, FDR<0.05:  29 
# Adjusted, pBonf<0.05:  8 
# Adjusted, lambda:  1.082819 

# Number of DMRs identified:   18 

DMP_Cu_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  18618 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.021546 
 
# Number of identified DMR:  0

rm(DMP_Cu_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
1551	cg00082497	-0.25 (-0.36 ,-0.15)	-5.32	2.8e-06	0.0375331	1.0000	chr1	32802133	MARCKSL1
2216	cg00116766	0.42 (0.28 ,0.56)	2.04	0.0e+00	0.0013289	0.0021	chr16	9857614	GRIN2A;GRIN2A;GRIN2A
15593	cg00908120	0.52 (0.33 ,0.7)	6.26	1.0e-07	0.0056610	0.0509	chr16	72872925	ZFHX3;ZFHX3
36122	cg02155957	0.38 (0.23 ,0.53)	3.25	7.0e-07	0.0150267	0.2705	chr1	46930731
66105	cg04015129	0.7 (0.44 ,0.96)	4.28	3.0e-07	0.0080222	0.1043	chr10	1058036	GTPBP4
76780	cg04692924	-0.42 (-0.59 ,-0.26)	-6.61	1.0e-06	0.0191351	0.4018	chr1	161720042	DUSP12
82479	cg05051957	-0.45 (-0.63 ,-0.28)	-5.60	4.0e-07	0.0105360	0.1686	chr8	141522459	CHRAC1;CHRAC1
96056	cg05955013	-0.4 (-0.55 ,-0.24)	-6.28	4.0e-07	0.0105360	0.1624	chr17	45056646	RPRML
107200	cg06723863	-0.26 (-0.36 ,-0.15)	-5.98	1.8e-06	0.0275171	0.7154	chr16	68270129	ESRP2;ESRP2
117957	cg07380021	-0.51 (-0.69 ,-0.32)	-5.42	1.0e-07	0.0056342	0.0451	chr1	206755252	RASSF5;RASSF5;RASSF5
124637	cg07831553	0.61 (0.36 ,0.86)	3.37	2.5e-06	0.0358634	1.0000	chr19	48796974
132730	cg08370347	0.51 (0.3 ,0.72)	3.91	1.7e-06	0.0266105	0.6653	chr5	171571793	STK10
157990	cg10145926	0.61 (0.39 ,0.84)	5.31	2.0e-07	0.0061658	0.0678	chr14	95875792	C14orf139
165306	cg10653573	0.82 (0.49 ,1.15)	5.43	1.4e-06	0.0251851	0.5541	chr8	141347297	TRAPPC9;TRAPPC9
168880	cg10923018	0.24 (0.16 ,0.32)	2.75	0.0e+00	0.0026797	0.0134	chr6	31743769	C6orf27
178008	cg11608893	0.61 (0.36 ,0.86)	6.05	1.6e-06	0.0266105	0.6420	chr6	32059542	TNXB
184513	cg12067421	-0.46 (-0.62 ,-0.31)	2.01	0.0e+00	0.0015700	0.0047	chr1	203246482
202444	cg13434714	-0.42 (-0.58 ,-0.26)	-5.77	8.0e-07	0.0172634	0.3280	chr12	6936787	LEPREL2
238372	cg15790767	1.05 (0.67 ,1.42)	3.84	1.0e-07	0.0042467	0.0297	chr6	13431216	GFOD1
257054	cg17143270	0.82 (0.51 ,1.14)	5.74	4.0e-07	0.0105360	0.1677	chr1	91532819
272331	cg18299835	-0.23 (-0.33 ,-0.14)	-4.13	2.1e-06	0.0304573	0.8223	chr19	13207445	NFIX
277756	cg18714712	-0.54 (-0.72 ,-0.36)	-5.97	0.0e+00	0.0013289	0.0027	chr19	49866917	DKKL1;TEAD2
288096	cg19532212	0.49 (0.31 ,0.67)	4.46	3.0e-07	0.0080222	0.1016	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C
292461	cg19842134	-0.29 (-0.4 ,-0.17)	-3.53	9.0e-07	0.0178044	0.3561	chr12	54070591	ATP5G2;ATP5G2
299106	cg20365618	-0.24 (-0.34 ,-0.15)	0.42	1.5e-06	0.0262342	0.6034	chr10	121578384	INPP5F;INPP5F
338217	cg23477849	0.28 (0.19 ,0.38)	4.88	0.0e+00	0.0020266	0.0081	chr19	5698492	LONP1
370410	cg25954729	-0.22 (-0.3 ,-0.14)	-6.34	2.0e-07	0.0059844	0.0598	chr11	66610784	RCE1;C11orf80;RCE1
381104	cg26708724	0.66 (0.41 ,0.92)	6.73	5.0e-07	0.0120529	0.2049	chr4	187509785	FAT1
393045	cg27565067	0.48 (0.31 ,0.65)	6.20	0.0e+00	0.0029493	0.0177	chr17	149484	RPH3AL

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
22	45704901	45705265	0.0e+00	364	0.0e+00	0.0000000	7
20	35169538	35169886	0.0e+00	348	0.0e+00	0.0000000	6
16	66304366	66304585	0.0e+00	219	0.0e+00	0.0000001	3
10	121578136	121578639	0.0e+00	503	0.0e+00	0.0000001	4
12	54070516	54070610	0.0e+00	94	0.0e+00	0.0000006	5
16	8806530	8806756	0.0e+00	226	0.0e+00	0.0000004	7
17	149483	149488	0.0e+00	5	0.0e+00	0.0001527	2
6	1604012	1604212	0.0e+00	200	0.0e+00	0.0000163	5
20	3052114	3052483	0.0e+00	369	0.0e+00	0.0000189	9
17	1395863	1396123	0.0e+00	260	0.0e+00	0.0000409	5
19	55660590	55660625	0.0e+00	35	0.0e+00	0.0003053	4
15	100048370	100048500	0.0e+00	130	1.0e-07	0.0001014	3
2	130345204	130345405	0.0e+00	201	1.0e-07	0.0000974	3
17	47091977	47092178	1.0e-07	201	1.0e-07	0.0001424	4
19	50194119	50194252	1.0e-07	133	1.0e-07	0.0002345	5
13	100310161	100310405	1.0e-07	244	1.0e-07	0.0001709	4
11	19736149	19736333	1.0e-07	184	1.0e-07	0.0002923	5
1	207082827	207082900	1.1e-06	73	1.1e-06	0.0059448	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, female

DMP_Cu_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  19233 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16152 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.952899 
 
# Number of DMRs identified:   11 

DMP_Cu_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  12980 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8014961 
 
# Number of DMRs identified:   2 

rm(DMP_Cu_F_age7_cordoverlap);gc

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	32063900	32064842	0.0000000	942	0.0000000	0.0000000	33
5	191295	191806	0.0000000	511	0.0000000	0.0000000	9
15	81426346	81426610	0.0000000	264	0.0000000	0.0000002	7
11	73357094	73357396	0.0000000	302	0.0000001	0.0000556	7
2	74875226	74875536	0.0000001	310	0.0000001	0.0000788	7
21	37442288	37442476	0.0000001	188	0.0000002	0.0002543	3
17	1395863	1396123	0.0000001	260	0.0000002	0.0001967	5
1	120174148	120174361	0.0000001	213	0.0000002	0.0002411	2
8	95962351	95962383	0.0000017	32	0.0000021	0.0210023	4
19	23941312	23941438	0.0001402	126	0.0001543	0.3553439	3
6	31734291	31734401	0.0007630	110	0.0007630	0.9352574	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, male

DMP_Cu_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  8255 
# Unadjusted, FDR<0.05:  32 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  11939 
# Adjusted, FDR<0.05:  49 
# Adjusted, pBonf<0.05:  14 
# Adjusted, lambda:  0.7284168 
 
# Number of DMRs identified:   14 

DMP_Cu_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  14082 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8571026 
 
# Number of DMRs identified:   10 

rm(DMP_Cu_M_age7_cordoverlap);gc

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
15593	cg00908120	0.71 (0.47 ,0.96)	6.29	1.0e-07	0.0017621	0.0229	chr16	72872925	ZFHX3;ZFHX3
17338	cg01007589	0.91 (0.59 ,1.23)	4.79	1.0e-07	0.0030119	0.0422	chr19	49894178	CCDC155
18335	cg01063965	-0.27 (-0.37 ,-0.17)	-6.44	4.0e-07	0.0086883	0.1564	chr11	695461	TMEM80;TMEM80;DEAF1;DEAF1
24635	cg01447660	0.39 (0.23 ,0.54)	-0.92	1.9e-06	0.0224235	0.7624	chr2	69152678
25210	cg01485439	0.51 (0.31 ,0.7)	3.65	7.0e-07	0.0130637	0.2613	chr11	67225937	CABP4
36122	cg02155957	0.49 (0.29 ,0.68)	3.22	1.6e-06	0.0201772	0.6255	chr1	46930731
36678	cg02196294	-0.26 (-0.37 ,-0.15)	-5.41	4.2e-06	0.0349929	1.0000	chr6	39197260	KCNK5
41497	cg02490920	0.37 (0.24 ,0.51)	1.34	3.0e-07	0.0075004	0.1275	chr3	50304406	SEMA3B;SEMA3B
49479	cg02968175	0.31 (0.2 ,0.42)	5.76	2.0e-07	0.0053540	0.0857	chr16	4690020	MGRN1;MGRN1;MGRN1;MGRN1
61452	cg03717239	0.3 (0.18 ,0.42)	0.51	2.7e-06	0.0271495	1.0000	chr8	145574318
62678	cg03790745	0.28 (0.16 ,0.39)	5.56	3.5e-06	0.0321103	1.0000	chr11	63679432	RCOR2
66105	cg04015129	0.85 (0.56 ,1.13)	4.27	0.0e+00	0.0010425	0.0090	chr10	1058036	GTPBP4
72385	cg04406071	-0.3 (-0.41 ,-0.19)	-6.07	5.0e-07	0.0096730	0.1838	chr17	59489784	C17orf82
76780	cg04692924	-0.6 (-0.83 ,-0.37)	-6.58	1.0e-06	0.0158267	0.3957	chr1	161720042	DUSP12
82479	cg05051957	-0.62 (-0.86 ,-0.37)	-5.61	1.3e-06	0.0178448	0.5175	chr8	141522459	CHRAC1;CHRAC1
96056	cg05955013	-0.47 (-0.67 ,-0.28)	-6.30	2.7e-06	0.0271495	1.0000	chr17	45056646	RPRML
117957	cg07380021	-0.67 (-0.89 ,-0.45)	-5.43	0.0e+00	0.0010425	0.0047	chr1	206755252	RASSF5;RASSF5;RASSF5
132177	cg08329655	-0.44 (-0.6 ,-0.27)	-5.88	1.1e-06	0.0163083	0.4470	chr11	7534677	PPFIBP2
133940	cg08459368	0.58 (0.35 ,0.81)	2.70	1.7e-06	0.0203444	0.6510	chr11	61974948	SCGB2A1
138326	cg08760128	0.31 (0.19 ,0.42)	6.73	9.0e-07	0.0155789	0.3739	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1
159790	cg10266648	1.06 (0.69 ,1.43)	5.98	1.0e-07	0.0017511	0.0210	chr2	106560529
168880	cg10923018	0.35 (0.24 ,0.46)	2.73	0.0e+00	0.0004255	0.0009	chr6	31743769	C6orf27
178008	cg11608893	0.95 (0.64 ,1.26)	6.08	0.0e+00	0.0010425	0.0042	chr6	32059542	TNXB
186947	cg12243007	0.46 (0.27 ,0.64)	-0.77	3.3e-06	0.0310915	1.0000	chr17	184018	RPH3AL
202444	cg13434714	-0.68 (-0.87 ,-0.48)	-5.78	0.0e+00	0.0000612	0.0001	chr12	6936787	LEPREL2
211983	cg13989834	0.55 (0.34 ,0.76)	3.14	9.0e-07	0.0146279	0.3364	chr9	134400392	UCK1;UCK1
232975	cg15389183	-0.22 (-0.31 ,-0.13)	-6.19	3.3e-06	0.0310915	1.0000	chr14	102829482	TECPR2;CINP
238372	cg15790767	1.16 (0.68 ,1.64)	3.86	4.2e-06	0.0349929	1.0000	chr6	13431216	GFOD1
242146	cg16068812	-1.01 (-1.42 ,-0.6)	-4.27	2.5e-06	0.0271495	0.9973	chr21	44528396	U2AF1;U2AF1;U2AF1
248112	cg16496814	0.28 (0.17 ,0.39)	5.22	1.1e-06	0.0163083	0.4461	chr11	9778721
250632	cg16656826	0.33 (0.2 ,0.45)	0.14	7.0e-07	0.0135857	0.2853	chr5	159343871	ADRA1B;ADRA1B
277216	cg18670846	0.73 (0.43 ,1.03)	-2.30	3.7e-06	0.0324333	1.0000	chr2	68917482
277756	cg18714712	-0.73 (-0.97 ,-0.48)	-5.95	0.0e+00	0.0010425	0.0094	chr19	49866917	DKKL1;TEAD2
281545	cg19005275	0.68 (0.45 ,0.92)	4.29	1.0e-07	0.0017511	0.0204	chr12	113588263	CCDC42B
288096	cg19532212	0.7 (0.45 ,0.95)	4.42	2.0e-07	0.0051395	0.0771	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C
299106	cg20365618	-0.35 (-0.47 ,-0.23)	0.40	0.0e+00	0.0010425	0.0063	chr10	121578384	INPP5F;INPP5F
301945	cg20597842	0.99 (0.59 ,1.4)	5.88	3.1e-06	0.0308990	1.0000	chr12	7818585	APOBEC1
311691	cg21373263	0.79 (0.48 ,1.09)	3.29	8.0e-07	0.0146279	0.3254	chr10	126751982	CTBP2;CTBP2
317735	cg21864868	0.66 (0.4 ,0.91)	4.22	1.2e-06	0.0163083	0.4566	chr17	46673002	LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
322216	cg22240394	1.07 (0.65 ,1.49)	6.82	1.4e-06	0.0183349	0.5500	chr3	186211630
322745	cg22286640	-0.78 (-1.1 ,-0.46)	-4.65	4.3e-06	0.0349929	1.0000	chr8	67026828
336099	cg23312431	0.34 (0.2 ,0.47)	-0.37	1.8e-06	0.0211836	0.6991	chr21	45773997	TRPM2
338217	cg23477849	0.39 (0.25 ,0.52)	4.90	1.0e-07	0.0017511	0.0202	chr19	5698492	LONP1
352329	cg24543538	0.84 (0.5 ,1.17)	3.22	2.0e-06	0.0228393	0.7994	chr2	241569846	GPR35
365034	cg25514328	-0.47 (-0.66 ,-0.27)	-4.77	3.6e-06	0.0321103	1.0000	chr17	78549324	RPTOR;RPTOR
370410	cg25954729	-0.31 (-0.41 ,-0.21)	-6.37	0.0e+00	0.0010425	0.0053	chr11	66610784	RCE1;C11orf80;RCE1
378724	cg26543311	1.1 (0.64 ,1.56)	7.17	4.4e-06	0.0357043	1.0000	chr12	48875427	C12orf54
381104	cg26708724	0.95 (0.63 ,1.27)	6.72	0.0e+00	0.0010425	0.0088	chr4	187509785	FAT1
392164	cg27503275	0.43 (0.26 ,0.61)	4.12	2.7e-06	0.0271495	1.0000	chr6	3880016

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	121578136	121578846	0.0000000	710	0.0000000	0.0000000	5
22	45704901	45705265	0.0000000	364	0.0000000	0.0000000	7
21	45773781	45773997	0.0000000	216	0.0000000	0.0000009	2
4	24796918	24797176	0.0000000	258	0.0000000	0.0000093	6
19	50194119	50194252	0.0000000	133	0.0000000	0.0000207	5
17	70723226	70723386	0.0000000	160	0.0000000	0.0000504	2
20	35169593	35169886	0.0000000	293	0.0000001	0.0000373	5
17	78549323	78549371	0.0000000	48	0.0000001	0.0003164	3
3	16216093	16216215	0.0000001	122	0.0000001	0.0002044	4
14	78447480	78447640	0.0000001	160	0.0000001	0.0001737	3
17	149483	149488	0.0000001	5	0.0000002	0.0111041	2
10	135051232	135051351	0.0000006	119	0.0000007	0.0020801	7
12	54070516	54070591	0.0000107	75	0.0000115	0.0546485	4
16	8806689	8806756	0.0003889	67	0.0003889	0.8987147	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_manhattan_DMP_adj.png")

Hg

DMP_Hg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk')

# Unadjusted, N =  326 
# Unadjusted, p<0.05:  37293 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  326 
# Adjusted, p<0.05:  26572 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.213221 
 
# Number of DMRs identified:   4 

DMP_Hg_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  186 
# Adjusted, p<0.05:  25003 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.148742 
 
# Number of DMRs identified:   3 

rm(DMP_Hg_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	46681110	46681401	0.00e+00	291	0.00e+00	0.0000009	6
6	31846768	31847009	0.00e+00	241	0.00e+00	0.0000034	9
10	131843516	131843798	0.00e+00	282	0.00e+00	0.0000112	4
3	42977888	42978026	2.93e-05	138	2.93e-05	0.0802830	4

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, female

DMP_Hg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk')

# Unadjusted, N =  154 
# Unadjusted, p<0.05:  35686 
# Unadjusted, FDR<0.05:  156 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  154 
# Adjusted, p<0.05:  15090 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8796583 
 
# Number of DMRs identified:   3 

DMP_Hg_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  83 
# Adjusted, p<0.05:  11644 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7673862 
 
# Number of DMRs identified:   2 

rm(DMP_Hg_F_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
12	47219625	47220092	0e+00	467	0e+00	0.0000001	12
4	165877874	165878136	0e+00	262	0e+00	0.0000008	6
7	27143234	27143478	1e-07	244	1e-07	0.0001227	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, male

DMP_Hg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk')

# Unadjusted, N =  172 
# Unadjusted, p<0.05:  22412 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  172 
# Adjusted, p<0.05:  24091 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.207859 
 
# Number of DMRs identified:   9 

DMP_Hg_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  103 
# Adjusted, p<0.05:  24791 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.169208 

# Number of DMRs identified:   5 

rm(DMP_Hg_M_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	31846768	31847009	0.0000000	241	0.0000000	0.0000000	9
11	18477152	18477534	0.0000000	382	0.0000000	0.0000001	7
11	18433499	18433887	0.0000000	388	0.0000000	0.0000001	5
5	502290	502571	0.0000000	281	0.0000000	0.0000004	3
6	33282735	33283162	0.0000000	427	0.0000000	0.0000011	20
14	104690039	104690244	0.0000000	205	0.0000000	0.0000129	5
1	147737015	147737207	0.0000001	192	0.0000002	0.0002762	4
1	2345151	2345410	0.0000002	259	0.0000002	0.0002468	8
1	117317981	117318133	0.0011583	152	0.0011583	0.9505995	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_manhattan_DMP_adj.png")

Mg

DMP_Mg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  18232 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15821 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8746056 
 
# Number of DMRs identified:   5 

DMP_Mg_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  16543 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9351369 
 
# Number of DMRs identified:   2 

rm(DMP_Mg_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
20	3051953	3052345	0.0000000	392	0.0000000	0.0000000	9
6	31543539	31543686	0.0000000	147	0.0000000	0.0000353	8
2	240196768	240196996	0.0000001	228	0.0000001	0.0000921	3
11	368564	368712	0.0000014	148	0.0000017	0.0035951	7
6	10884093	10884140	0.0007239	47	0.0007239	0.9977073	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, female

DMP_Mg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  33977 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  20594 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.079708 
 
# Number of DMRs identified:   2 

DMP_Mg_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  17171 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9523752 
 
# Number of DMRs identified:   3 

rm(DMP_Mg_F_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
2	240196876	240196996	0.0000008	120	0.0000017	0.0027396	2
6	10884093	10884140	0.0001867	47	0.0001867	0.7913380	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, male

DMP_Mg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  9395 
# Unadjusted, FDR<0.05:  7 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13551 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8048792 

# Number of identified DMR:  2

DMP_Mg_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  14864 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8507625 
 
# Number of DMRs identified:   5 

rm(DMP_Mg_M_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
202444	cg13434714	-0.6 (-0.79 ,-0.41)	-5.78	0	0.0016633	0.0017	chr12	6936787	LEPREL2
277216	cg18670846	0.84 (0.56 ,1.12)	-2.30	0	0.0030248	0.0060	chr2	68917482
381104	cg26708724	0.89 (0.58 ,1.19)	6.72	0	0.0059299	0.0178	chr4	187509785	FAT1

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
5	23507449	23507656	0	207	0	6.62e-05	5
17	37123668	37123949	0	281	0	5.24e-05	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_manhattan_DMP_adj.png")

Mn

DMP_Mn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  27983 
# Unadjusted, FDR<0.05:  6 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  37788 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.339163 
 
# Number of DMRs identified:   10 

DMP_Mn_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk_beta')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  34004 
# Unadjusted, FDR<0.05:  2096 
# Unadjusted, pBonf<0.05:  39 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  42632 
# Adjusted, FDR<0.05:  5339 
# Adjusted, pBonf<0.05:  75 
# Adjusted, lambda:  1.240793 
 
# Number of DMRs identified:   121 

DMP_Mn_age7_beta[[3]][DMP_Mn_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg02042823 0.7500762 0.1418274 1.358325

rm(DMP_Mn_age7_beta);gc()

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  39204 
# Adjusted, FDR<0.05:  65 
# Adjusted, pBonf<0.05:  8 
# Adjusted, lambda:  1.310818 
 
# Number of DMRs identified:   9 

rm(DMP_Mn_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
13985	cg00808511	0.18 (0.11 ,0.25)	2.86	1.5e-06	0.0441289	0.5737	chr16	52495237	TOX3;TOX3
61437	cg03716590	0.18 (0.11 ,0.25)	5.09	9.0e-07	0.0357372	0.3580	chr7	95435309	DYNC1I1;DYNC1I1;DYNC1I1
90890	cg05613017	0.2 (0.12 ,0.28)	5.33	5.0e-07	0.0310721	0.2156	chr12	65589446	LEMD3;LEMD3
153815	cg09856068	-0.11 (-0.16 ,-0.07)	-4.37	8.0e-07	0.0357372	0.3012	chr5	170878246	FGF18
170758	cg11063328	-0.16 (-0.22 ,-0.1)	-6.02	6.0e-07	0.0310721	0.2175	chr11	18343203	GTF2H1;HPS5;HPS5;HPS5;GTF2H1
209344	cg13834844	-0.1 (-0.14 ,-0.06)	-5.14	1.0e-07	0.0138786	0.0555	chr10	102415320
216559	cg14252211	0.2 (0.13 ,0.26)	5.85	0.0e+00	0.0023306	0.0047	chr1	25919394
286458	cg19407717	0.31 (0.22 ,0.4)	4.03	0.0e+00	0.0000169	0.0000	chr2	1544120	TPO;TPO;TPO;TPO
286677	cg19425870	-0.15 (-0.21 ,-0.09)	-6.46	1.0e-06	0.0357372	0.3931	chr11	3876808	STIM1
326256	cg22586726	0.27 (0.16 ,0.38)	-0.97	1.3e-06	0.0424978	0.5100	chr10	134150542	LRRC27;LRRC27;LRRC27;LRRC27;LRRC27
347861	cg24196240	0.33 (0.21 ,0.45)	5.25	1.0e-07	0.0114167	0.0343	chr21	36096009	NCRNA00160
359777	cg25101184	0.25 (0.15 ,0.34)	3.38	8.0e-07	0.0357372	0.3286	chr14	56231604	RPL13AP3
386595	cg27095984	-0.19 (-0.26 ,-0.12)	5.27	3.0e-07	0.0216665	0.1083	chr13	21652115

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	134150488	134150760	0.0000000	272	0.0000000	0.0000000	7
19	21657528	21657756	0.0000000	228	0.0000000	0.0000002	4
16	30572738	30573013	0.0000000	275	0.0000000	0.0000004	5
10	45406680	45406847	0.0000000	167	0.0000000	0.0000545	3
16	73100425	73100510	0.0000000	85	0.0000000	0.0001310	2
11	76839190	76839476	0.0000000	286	0.0000000	0.0000395	4
20	61659979	61660250	0.0000001	271	0.0000001	0.0001260	2
15	91473290	91473386	0.0000226	96	0.0000282	0.0885929	3
10	35484767	35484824	0.0003062	57	0.0003402	0.8798961	3
10	530950	531098	0.0019955	148	0.0019955	0.9951256	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, female

DMP_Mn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  28256 
# Unadjusted, FDR<0.05:  3 
# Unadjusted, pBonf<0.05:  3 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  39831 
# Adjusted, FDR<0.05:  6 
# Adjusted, pBonf<0.05:  2 
# Adjusted, lambda:  1.354546 
 
# Number of DMRs identified:   1

DMP_Mn_F_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_F_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk_beta')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  34431 
# Unadjusted, FDR<0.05:  3379 
# Unadjusted, pBonf<0.05:  42 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  43301 
# Adjusted, FDR<0.05:  7595 
# Adjusted, pBonf<0.05:  69 
# Adjusted, lambda:  1.248445 
 
# Number of DMRs identified:   171 

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg00954161',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg00954161 1.333573 0.6920163 1.975131

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg11161853',c(2:4)]*100
                # logFC        CI.L       CI.R
# cg11161853 0.00902998 -0.05582495 0.07388491

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg23903787',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg23903787 2.035622 0.7851984 3.286046

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg19908812',c(2:4)]*100
                 # logFC       CI.L      CI.R
# cg19908812 -0.03226102 -0.3388754 0.2743534

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg26462130',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg26462130 0.9842899 0.6837261 1.284854

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg08904630',c(2:4)]*100
               # logFC      CI.L      CI.R
# cg08904630 0.4763335 0.3358858 0.6167811

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg22799518',c(2:4)]*100
                # logFC       CI.L       CI.R
# cg22799518 -0.2005144 -0.4265598 0.02553097

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg01744822',c(2:4)]*100
               # logFC      CI.L      CI.R
# cg01744822 -1.662075 -2.293577 -1.030573

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg15712310',c(2:4)]*100
                # logFC      CI.L        CI.R
# cg15712310 -0.9650864 -1.858607 -0.07156615

rm(DMP_Mn_F_age7_beta);gc()

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  45254 
# Adjusted, FDR<0.05:  433 
# Adjusted, pBonf<0.05:  7 
# Adjusted, lambda:  1.388295 
 
# Number of DMRs identified:   25 

rm(DMP_Mn_F_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
48627	cg02920176	0.28 (0.17 ,0.38)	5.13	7e-07	0.0478732	0.2859	chr7	36404389	KIAA0895;KIAA0895
90890	cg05613017	0.26 (0.16 ,0.36)	5.32	7e-07	0.0478732	0.2854	chr12	65589446	LEMD3;LEMD3
170758	cg11063328	-0.26 (-0.33 ,-0.18)	-6.00	0e+00	0.0003803	0.0005	chr11	18343203	GTF2H1;HPS5;HPS5;HPS5;GTF2H1
250921	cg16675029	-0.11 (-0.15 ,-0.07)	-6.42	7e-07	0.0478732	0.2872	chr8	6565876	AGPAT5
286677	cg19425870	-0.25 (-0.32 ,-0.17)	-6.45	0e+00	0.0003803	0.0008	chr11	3876808	STIM1
324070	cg22396353	-0.15 (-0.2 ,-0.1)	-6.10	1e-07	0.0170936	0.0513	chr22	46692687	GTSE1;GTSE1;CN5H6.4

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	3849410	3849690	5e-07	280	5e-07	0.0007357	10

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, male

DMP_Mn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  14905 
# Unadjusted, FDR<0.05:  27 
# Unadjusted, pBonf<0.05:  9 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  18986 
# Adjusted, FDR<0.05:  30 
# Adjusted, pBonf<0.05:  13 
# Adjusted, lambda:  0.9800403 
 
# Number of DMRs identified:   14 

DMP_Mn_M_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_M_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk_beta')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  14417 
# Unadjusted, FDR<0.05:  227 
# Unadjusted, pBonf<0.05:  82 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  18971 
# Adjusted, FDR<0.05:  257 
# Adjusted, pBonf<0.05:  85 
# Adjusted, lambda:  0.9273041 
 
# Number of DMRs identified:   27 

DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg03763518',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg03763518 -3.025927 -4.557014 -1.49484

DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg02042823 1.815752 0.5050111 3.126493

rm(DMP_Mn_M_age7_beta);gc()

# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  15442 
# Adjusted, FDR<0.05:  45 
# Adjusted, pBonf<0.05:  12 
# Adjusted, lambda:  0.8201768 

# Number of DMRs identified:   16 

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
56695	cg03425412	-0.22 (-0.31 ,-0.14)	-5.94	1.1e-06	0.0200355	0.4408	chr20	21500337
68153	cg04143120	0.41 (0.27 ,0.55)	6.79	0.0e+00	0.0009703	0.0068	chr11	72968848
79809	cg04885068	0.19 (0.12 ,0.25)	6.47	1.0e-07	0.0034580	0.0386	chr1	9099298	SLC2A5;SLC2A5
82300	cg05041382	-0.12 (-0.17 ,-0.07)	-6.39	2.4e-06	0.0357914	0.9313	chr13	50366546	KPNA3
85445	cg05249026	-0.16 (-0.22 ,-0.1)	-2.36	3.0e-07	0.0071381	0.1213	chr16	11031524	DEXI
97510	cg06051716	0.36 (0.24 ,0.47)	6.49	0.0e+00	0.0002792	0.0015	chr6	169225783
107728	cg06756211	-0.21 (-0.27 ,-0.14)	-6.05	0.0e+00	0.0002792	0.0017	chr1	223936799	CAPN2;CAPN2
109948	cg06883949	-0.12 (-0.17 ,-0.07)	-6.47	8.0e-07	0.0151676	0.3034	chr4	1795240	FGFR3;FGFR3;FGFR3
128092	cg08072480	-0.14 (-0.19 ,-0.08)	-6.61	2.0e-06	0.0320210	0.7829	chr11	65292666	SCYL1;SCYL1
157031	cg10088075	-0.11 (-0.16 ,-0.07)	-6.21	3.8e-06	0.0499734	1.0000	chr16	30407103	ZNF48;ZNF48
176390	cg11480534	0.4 (0.24 ,0.55)	5.84	9.0e-07	0.0173628	0.3646	chr11	62255850	AHNAK
176843	cg11521780	-0.14 (-0.18 ,-0.09)	-5.77	0.0e+00	0.0015624	0.0125	chr12	53693949	C12orf10
180100	cg11755803	0.4 (0.24 ,0.56)	5.79	1.7e-06	0.0288393	0.6633	chr12	129000542	TMEM132C
192975	cg12700904	-0.1 (-0.14 ,-0.06)	-5.94	2.9e-06	0.0388460	1.0000	chr3	13590720	FBLN2;FBLN2
194538	cg12828656	-0.15 (-0.2 ,-0.1)	-0.50	0.0e+00	0.0002792	0.0012	chr5	132577108	FSTL4
209344	cg13834844	-0.15 (-0.22 ,-0.09)	-5.13	2.0e-06	0.0320210	0.8005	chr10	102415320
209541	cg13848566	-0.17 (-0.22 ,-0.11)	-6.36	2.0e-07	0.0041615	0.0624	chr9	89561175	GAS1
214672	cg14149680	-0.29 (-0.38 ,-0.2)	-6.35	0.0e+00	0.0001372	0.0004	chr11	2187632	TH;TH;TH
249118	cg16560774	-0.17 (-0.22 ,-0.11)	-6.46	0.0e+00	0.0018682	0.0168	chr17	79373381	BAHCC1
286458	cg19407717	0.5 (0.35 ,0.64)	4.03	0.0e+00	0.0000364	0.0001	chr2	1544120	TPO;TPO;TPO;TPO
287817	cg19511862	-0.1 (-0.14 ,-0.06)	-6.26	5.0e-07	0.0106449	0.2023	chr12	125478458	BRI3BP
289598	cg19641404	-0.11 (-0.16 ,-0.07)	-5.87	2.5e-06	0.0357914	0.9762	chr2	232826272	DIS3L2
299702	cg20414082	0.26 (0.16 ,0.36)	3.20	4.0e-07	0.0085706	0.1543	chr1	203002593
300828	cg20504533	-0.22 (-0.28 ,-0.15)	-5.85	0.0e+00	0.0000364	0.0001	chr17	15848253	ADORA2B;ADORA2B
326031	cg22563312	-0.17 (-0.22 ,-0.11)	-6.27	1.0e-07	0.0034580	0.0450	chr5	179334739	TBC1D9B;TBC1D9B
327739	cg22702772	-0.15 (-0.2 ,-0.1)	-6.69	1.0e-07	0.0034580	0.0430	chr3	48699012	CELSR3
347861	cg24196240	0.42 (0.27 ,0.56)	5.27	2.0e-07	0.0041615	0.0617	chr21	36096009	NCRNA00160
357841	cg24948962	-0.22 (-0.29 ,-0.14)	-5.44	1.0e-07	0.0034580	0.0385	chr18	2906032	EMILIN2
360532	cg25152909	0.43 (0.27 ,0.58)	6.08	2.0e-07	0.0043902	0.0702	chr5	172566090	C5orf41
364427	cg25466588	-0.09 (-0.13 ,-0.06)	-5.90	2.5e-06	0.0357914	1.0000	chr3	23958904	NKIRAS1;RPL15

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
1	161008461	161008977	0.0000000	516	0.0000000	0.0000000	8
19	21657528	21658001	0.0000000	473	0.0000000	0.0000000	5
19	10736005	10736117	0.0000000	112	0.0000000	0.0000055	5
20	5485244	5485511	0.0000000	267	0.0000000	0.0000036	6
4	79971176	79971432	0.0000000	256	0.0000000	0.0000079	4
20	35169593	35169886	0.0000000	293	0.0000000	0.0000081	5
1	9099280	9099462	0.0000001	182	0.0000002	0.0001641	3
6	26018002	26018185	0.0000001	183	0.0000002	0.0002514	6
16	30572738	30573013	0.0000001	275	0.0000002	0.0001883	5
3	39543966	39544192	0.0000032	226	0.0000045	0.0055785	2
15	91473090	91473365	0.0000066	275	0.0000084	0.0094606	4
19	12444612	12444741	0.0000102	129	0.0000119	0.0307855	5
6	37616597	37616686	0.0000933	89	0.0001005	0.3386856	2
2	3642628	3642634	0.0032946	6	0.0032946	1.0000000	2

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_manhattan_DMP_adj.png")

Pb

DMP_Pb_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  13157 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19598 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.056675 

# Number of DMRs identified:   6 

DMP_Pb_age7[[3]] = NULL

# limma on Beta-values
DMP_Pb_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk_beta')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  13578 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20646 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  1.092762 
 
# Number of DMRs identified:   6 

DMP_Pb_age7_beta[[3]][DMP_Pb_age7_beta[[3]]$cpg == 'cg20608990',c(2:4)]*100
               # logFC      CI.L       CI.R
# cg20608990 -1.564971 -2.725569 -0.4043731

rm(DMP_Pb_age7_beta);gc()

# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  43924 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.730948 
 
# Number of identified DMR:  0

rm(DMP_Pb_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	135051021	135051581	0e+00	560	0e+00	0.0000000	11
22	45704901	45705265	0e+00	364	0e+00	0.0000000	7
22	19746155	19746368	0e+00	213	0e+00	0.0000225	3
3	130745441	130745685	0e+00	244	0e+00	0.0000389	10
7	155283139	155283424	0e+00	285	1e-07	0.0000621	3
14	104690039	104690244	1e-07	205	1e-07	0.0002063	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, female

DMP_Pb_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  10571 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  12151 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7522295 
 
# Number of identified DMR:  0

DMP_Pb_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  15685 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9341139 
 
# Number of identified DMR:  0

rm(DMP_Pb_F_age7_cordoverlap);gc()

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, male

DMP_Pb_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  18362 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14153 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9440498 
 
# Number of DMRs identified:   4 

DMP_Pb_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  21607 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.165536 
 
# Number of DMRs identified:   6 

rm(DMP_Pb_M_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
6	33084769	33084985	0	216	0	1.00e-07	11
1	68512649	68513063	0	414	0	3.00e-07	7
6	31148369	31148748	0	379	0	2.70e-06	13
22	45704987	45705265	0	278	0	6.82e-05	5

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_manhattan_DMP_adj.png")

Se

DMP_Se_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  17270 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20324 
# Adjusted, FDR<0.05:  4 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.9736407 
 
# Number of DMRs identified:   3 

DMP_Se_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  16337 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8902786 
 
# Number of DMRs identified:   2

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
138326	cg08760128	0.2 (0.13 ,0.28)	6.73	4e-07	0.0460845	0.1487	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1
157990	cg10145926	0.55 (0.35 ,0.75)	5.31	1e-07	0.0286748	0.0573	chr14	95875792	C14orf139
202444	cg13434714	-0.42 (-0.57 ,-0.28)	-5.77	0e+00	0.0077289	0.0077	chr12	6936787	LEPREL2
381104	cg26708724	0.59 (0.36 ,0.81)	6.73	5e-07	0.0460845	0.1843	chr4	187509785	FAT1

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	47091977	47092178	0	201	0	4.00e-06	4
19	50194119	50194252	0	133	0	1.57e-05	5
6	49681177	49681391	0	214	0	2.89e-05	7

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_manhattan_DMP_adj.png")

Se, female

DMP_Se_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26254 
# Unadjusted, FDR<0.05:  9 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16049 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9296273 
 
# Number of DMRs identified:   3 

DMP_Se_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  16966 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9935428 
 
# Number of DMRs identified:   5 

rm(DMP_Se_F_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
10	38146245	38146671	0	426	0	4.00e-07	9
6	49681177	49681391	0	214	0	1.00e-06	7
10	38299241	38299574	0	333	0	1.83e-05	9

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_manhattan_DMP_adj.png")

Se, male

DMP_Se_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15593 
# Unadjusted, FDR<0.05:  42 
# Unadjusted, pBonf<0.05:  12 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13808 
# Adjusted, FDR<0.05:  20 
# Adjusted, pBonf<0.05:  6 
# Adjusted, lambda:  0.7972324 
 
# Number of DMRs identified:   3 

DMP_Se_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

Adjusted, N =  104 
Adjusted, p<0.05:  13747 
Adjusted, FDR<0.05:  0 
Adjusted, pBonf<0.05:  0 
Adjusted, lambda:  0.8042952 
 
Number of DMRs identified:   4 

rm(DMP_Se_M_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
5657	cg00326183	0.4 (0.24 ,0.56)	2.20	1.8e-06	0.0389133	0.7004	chr2	241808259	AGXT;AGXT
15593	cg00908120	0.6 (0.36 ,0.83)	6.29	1.1e-06	0.0299539	0.4194	chr16	72872925	ZFHX3;ZFHX3
17338	cg01007589	0.77 (0.47 ,1.07)	4.79	1.4e-06	0.0359853	0.5398	chr19	49894178	CCDC155
26849	cg01588060	-0.27 (-0.38 ,-0.17)	-5.90	8.0e-07	0.0259001	0.3108	chr6	2245749	GMDS;GMDS
76780	cg04692924	-0.59 (-0.8 ,-0.38)	-6.58	1.0e-07	0.0071719	0.0547	chr1	161720042	DUSP12
82479	cg05051957	-0.66 (-0.88 ,-0.44)	-5.61	0.0e+00	0.0015014	0.0046	chr8	141522459	CHRAC1;CHRAC1
107200	cg06723863	-0.34 (-0.47 ,-0.22)	-5.99	1.0e-07	0.0071719	0.0574	chr16	68270129	ESRP2;ESRP2
121260	cg07599133	-0.34 (-0.48 ,-0.21)	-5.96	1.8e-06	0.0389133	0.6939	chr19	35068628	LOC643719
175991	cg11443888	0.28 (0.17 ,0.39)	2.36	1.9e-06	0.0392822	0.7464	chr6	44244590	TMEM151B
178008	cg11608893	0.84 (0.55 ,1.12)	6.08	1.0e-07	0.0039836	0.0199	chr6	32059542	TNXB
186947	cg12243007	0.44 (0.27 ,0.61)	-0.77	1.0e-06	0.0289023	0.3757	chr17	184018	RPH3AL
195368	cg12897502	-0.84 (-1.16 ,-0.52)	6.10	6.0e-07	0.0204295	0.2247	chr8	67425316	C8orf46
202444	cg13434714	-0.63 (-0.81 ,-0.45)	-5.78	0.0e+00	0.0000186	0.0000	chr12	6936787	LEPREL2
250632	cg16656826	0.29 (0.18 ,0.41)	0.14	1.5e-06	0.0376409	0.6023	chr5	159343871	ADRA1B;ADRA1B
273355	cg18377660	0.71 (0.45 ,0.97)	5.65	2.0e-07	0.0089756	0.0808	chr1	57535755	DAB1
281545	cg19005275	0.59 (0.37 ,0.81)	4.29	4.0e-07	0.0162778	0.1628	chr12	113588263	CCDC42B
311691	cg21373263	0.82 (0.55 ,1.1)	3.29	0.0e+00	0.0015014	0.0060	chr10	126751982	CTBP2;CTBP2
359398	cg25067702	-0.64 (-0.87 ,-0.41)	-6.40	1.0e-07	0.0065970	0.0396	chr17	70723227	SLC39A11;SLC39A11
375884	cg26342676	0.61 (0.37 ,0.86)	4.56	2.3e-06	0.0454735	0.9095	chr14	37639757	SLC25A21;SLC25A21;LOC100129794
381104	cg26708724	1.01 (0.73 ,1.3)	6.72	0.0e+00	0.0000174	0.0000	chr4	187509785	FAT1

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	70723226	70723386	0e+00	160	0e+00	0.0000001	2
4	24796918	24797176	0e+00	258	0e+00	0.0000241	6
10	121578383	121578639	1e-07	256	1e-07	0.0001184	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_manhattan_DMP_adj.png")

Zn

DMP_Zn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  12854 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23322 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.103711 
 
# Number of DMRs identified:   13

DMP_Zn_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  189 
# Adjusted, p<0.05:  14814 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8661672 
 
# Number of DMRs identified:   5 

rm(DMP_Zn_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
1551	cg00082497	-0.28 (-0.38 ,-0.18)	-5.32	1.0e-07	0.0122297	0.0337	chr1	32802133	MARCKSL1
15593	cg00908120	0.49 (0.31 ,0.67)	6.26	3.0e-07	0.0170276	0.1166	chr16	72872925	ZFHX3;ZFHX3
66105	cg04015129	0.65 (0.4 ,0.91)	4.28	8.0e-07	0.0307007	0.3136	chr10	1058036	GTPBP4
90290	cg05573434	0.41 (0.26 ,0.57)	-3.15	3.0e-07	0.0170276	0.1192	chr4	7648540	SORCS2
107200	cg06723863	-0.25 (-0.35 ,-0.15)	-5.98	1.6e-06	0.0495322	0.6439	chr16	68270129	ESRP2;ESRP2
133940	cg08459368	0.59 (0.38 ,0.81)	2.65	1.0e-07	0.0122297	0.0395	chr11	61974948	SCGB2A1
165306	cg10653573	0.82 (0.5 ,1.14)	5.43	7.0e-07	0.0307007	0.2910	chr8	141347297	TRAPPC9;TRAPPC9
202444	cg13434714	-0.49 (-0.64 ,-0.33)	-5.77	0.0e+00	0.0012560	0.0013	chr12	6936787	LEPREL2
234745	cg15528091	-0.31 (-0.43 ,-0.19)	-6.36	9.0e-07	0.0307007	0.3391	chr19	18119069	ARRDC2;ARRDC2;ARRDC2
248112	cg16496814	0.21 (0.13 ,0.3)	5.21	6.0e-07	0.0299711	0.2398	chr11	9778721
281636	cg19011752	0.25 (0.15 ,0.34)	-2.54	9.0e-07	0.0307007	0.3684	chr21	45772638	TRPM2
338217	cg23477849	0.26 (0.16 ,0.36)	4.88	2.0e-07	0.0122297	0.0600	chr19	5698492	LONP1
370410	cg25954729	-0.22 (-0.29 ,-0.14)	-6.34	2.0e-07	0.0122297	0.0611	chr11	66610784	RCE1;C11orf80;RCE1

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
12	54070516	54070610	0.0000000	94	0.0000000	0.0000053	5
19	18118799	18119069	0.0000000	270	0.0000000	0.0000104	3
10	124638975	124639260	0.0000000	285	0.0000001	0.0000244	12
6	32063990	32064258	0.0000001	268	0.0000002	0.0000840	12
4	7648539	7648627	0.0000001	88	0.0000002	0.0003269	2
8	41655672	41655894	0.0000001	222	0.0000002	0.0002414	4
6	41168800	41169049	0.0000001	249	0.0000002	0.0002270	6
17	1395863	1396123	0.0000002	260	0.0000002	0.0002710	5
12	54385274	54385526	0.0000002	252	0.0000002	0.0002813	4
17	79503641	79503877	0.0000002	236	0.0000002	0.0003092	4
22	45704987	45705042	0.0000002	55	0.0000003	0.0015642	4
20	25129506	25129562	0.0000016	56	0.0000017	0.0113002	5
20	35169593	35169846	0.0004394	253	0.0004394	0.4960606	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, female

DMP_Zn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  12830 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  17367 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9501586 

# Number of DMRs identified:   1 

DMP_Zn_F_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  85 
# Adjusted, p<0.05:  12704 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7959756 
 
# Number of DMRs identified:   2 

rm(DMP_Zn_F_age7_cordoverlap);gc()

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
11	73357018	73357396	0	378	0	0	8

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, male

DMP_Zn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16787 
# Unadjusted, FDR<0.05:  36 
# Unadjusted, pBonf<0.05:  8 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14614 
# Adjusted, FDR<0.05:  37 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8610523 
 
# Number of DMRs identified:   16 

DMP_Zn_M_age7[[3]] = NULL

# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)

# Adjusted, N =  104 
# Adjusted, p<0.05:  14686 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.907332 
 
# Number of DMRs identified:   5

rm(DMP_Zn_M_age7_cordoverlap);gc()

FDR-significant DMPs

	cpg	logFC_CI	AveExpr	P.Value	adj.P.Val	adj.P.Val.bonf	chr	pos	gene
15593	cg00908120	0.79 (0.52 ,1.06)	6.29	0.0e+00	0.0059562	0.0162	chr16	72872925	ZFHX3;ZFHX3
17338	cg01007589	0.92 (0.56 ,1.28)	4.79	1.1e-06	0.0188947	0.4346	chr19	49894178	CCDC155
18335	cg01063965	-0.27 (-0.38 ,-0.16)	-6.44	4.3e-06	0.0462438	1.0000	chr11	695461	TMEM80;TMEM80;DEAF1;DEAF1
24635	cg01447660	0.42 (0.25 ,0.59)	-0.92	2.9e-06	0.0363415	1.0000	chr2	69152678
36678	cg02196294	-0.29 (-0.41 ,-0.17)	-5.41	4.0e-06	0.0443654	1.0000	chr6	39197260	KCNK5
41497	cg02490920	0.39 (0.24 ,0.54)	1.34	1.1e-06	0.0188947	0.4228	chr3	50304406	SEMA3B;SEMA3B
45187	cg02711608	0.54 (0.34 ,0.74)	-2.09	3.0e-07	0.0124570	0.1004	chr19	47287964	SLC1A5;SLC1A5;SLC1A5;SLC1A5
49479	cg02968175	0.33 (0.2 ,0.45)	5.76	7.0e-07	0.0136814	0.2736	chr16	4690020	MGRN1;MGRN1;MGRN1;MGRN1
55565	cg03352332	0.89 (0.55 ,1.22)	5.54	5.0e-07	0.0124570	0.1869	chr3	186360953	FETUB
66105	cg04015129	0.86 (0.55 ,1.18)	4.27	3.0e-07	0.0124570	0.0993	chr10	1058036	GTPBP4
71895	cg04374006	0.27 (0.16 ,0.37)	-0.27	2.3e-06	0.0311662	0.9038	chr19	33556395	RHPN2
72385	cg04406071	-0.32 (-0.45 ,-0.2)	-6.07	7.0e-07	0.0136814	0.2633	chr17	59489784	C17orf82
76780	cg04692924	-0.66 (-0.91 ,-0.41)	-6.58	8.0e-07	0.0148121	0.3111	chr1	161720042	DUSP12
82479	cg05051957	-0.65 (-0.92 ,-0.39)	-5.61	3.1e-06	0.0382640	1.0000	chr8	141522459	CHRAC1;CHRAC1
107200	cg06723863	-0.36 (-0.51 ,-0.21)	-5.99	3.3e-06	0.0382640	1.0000	chr16	68270129	ESRP2;ESRP2
117957	cg07380021	-0.66 (-0.91 ,-0.41)	-5.43	4.0e-07	0.0124570	0.1536	chr1	206755252	RASSF5;RASSF5;RASSF5
138326	cg08760128	0.36 (0.23 ,0.49)	6.73	1.0e-07	0.0124570	0.0590	chr16	4723507	MGRN1;MGRN1;MGRN1;MGRN1
159790	cg10266648	1.03 (0.62 ,1.44)	5.98	1.8e-06	0.0268172	0.6972	chr2	106560529
165306	cg10653573	1.41 (0.89 ,1.93)	5.37	3.0e-07	0.0124570	0.1021	chr8	141347297	TRAPPC9;TRAPPC9
168880	cg10923018	0.31 (0.18 ,0.43)	2.73	3.2e-06	0.0382640	1.0000	chr6	31743769	C6orf27
180170	cg11761483	-0.72 (-0.99 ,-0.45)	-5.60	4.0e-07	0.0124570	0.1584	chr17	70723386	SLC39A11;SLC39A11
202444	cg13434714	-0.83 (-1.04 ,-0.63)	-5.78	0.0e+00	0.0000001	0.0000	chr12	6936787	LEPREL2
216196	cg14230280	1.23 (0.74 ,1.72)	4.28	1.9e-06	0.0274435	0.7684	chr9	132502800	PTGES
248112	cg16496814	0.32 (0.2 ,0.44)	5.22	4.0e-07	0.0124570	0.1617	chr11	9778721
250632	cg16656826	0.35 (0.21 ,0.48)	0.14	1.9e-06	0.0273935	0.7396	chr5	159343871	ADRA1B;ADRA1B
268589	cg18037826	0.41 (0.26 ,0.57)	4.29	6.0e-07	0.0136814	0.2473	chr12	109273835	DAO
281545	cg19005275	0.75 (0.49 ,1.01)	4.29	0.0e+00	0.0059562	0.0179	chr12	113588263	CCDC42B
288096	cg19532212	0.75 (0.47 ,1.03)	4.42	3.0e-07	0.0124570	0.1355	chr17	56769430	TEX14;RAD51C;TEX14;RAD51C
311691	cg21373263	0.88 (0.55 ,1.21)	3.29	4.0e-07	0.0124570	0.1769	chr10	126751982	CTBP2;CTBP2
322216	cg22240394	1.22 (0.76 ,1.67)	6.82	5.0e-07	0.0124570	0.1825	chr3	186211630
324251	cg22413938	-0.39 (-0.55 ,-0.23)	-4.56	2.5e-06	0.0328489	0.9855	chr14	78447481
338217	cg23477849	0.38 (0.23 ,0.53)	4.90	1.6e-06	0.0255962	0.6399	chr19	5698492	LONP1
339781	cg23601521	0.8 (0.49 ,1.1)	4.87	6.0e-07	0.0136814	0.2553	chr2	50275179	NRXN1;NRXN1;NRXN1
370410	cg25954729	-0.3 (-0.41 ,-0.19)	-6.37	4.0e-07	0.0124570	0.1703	chr11	66610784	RCE1;C11orf80;RCE1
379632	cg26608798	0.4 (0.24 ,0.56)	0.58	1.6e-06	0.0255962	0.6283	chr16	33853544
381104	cg26708724	0.94 (0.58 ,1.29)	6.72	6.0e-07	0.0136814	0.2306	chr4	187509785	FAT1
392164	cg27503275	0.47 (0.28 ,0.66)	4.12	3.5e-06	0.0389303	1.0000	chr6	3880016

DMRs

chr	start	end	p	length	fdr	sidak	nprobe
17	70723226	70723386	0.0000000	160	0.0000000	0.0000015	2
10	121578136	121578639	0.0000000	503	0.0000000	0.0000016	4
4	24796918	24797176	0.0000000	258	0.0000000	0.0000052	6
14	78447480	78447640	0.0000000	160	0.0000000	0.0000104	3
19	50194119	50194252	0.0000000	133	0.0000000	0.0000187	5
4	186732836	186733060	0.0000000	224	0.0000000	0.0000223	7
14	76734326	76734605	0.0000000	279	0.0000000	0.0000293	5
21	45773781	45773997	0.0000000	216	0.0000001	0.0000492	2
5	135416204	135416613	0.0000000	409	0.0000001	0.0000444	9
11	63679431	63679637	0.0000001	206	0.0000001	0.0001629	2
20	62716331	62716606	0.0000001	275	0.0000002	0.0001988	4
17	78549323	78549371	0.0000002	48	0.0000002	0.0013191	3
5	1868136	1868357	0.0000004	221	0.0000005	0.0007748	4
22	45704987	45705042	0.0000016	55	0.0000018	0.0110616	4
5	176755392	176755449	0.0000113	57	0.0000120	0.0749153	2
2	88583556	88583805	0.0001352	249	0.0001352	0.1927662	3

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_manhattan_DMP_adj.png")